Make the TPR parser a bit faster #2804
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A function in the TPR parser calls list.pop thousands of times, which is slow. This commit avoids that exansive call. Taking the TPR from https://github.com/bioexcel/covid_modelling_simulation_data/tree/master/spike_protein/full_spike/trimer the parsing time on my computer goes from 25.6s to 9.39s. On a more pathological TPR file, it goes from 3 minutes to about 6s.
richardjgowers
approved these changes
Jun 29, 2020
Codecov Report
@@ Coverage Diff @@
## develop #2804 +/- ##
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- Coverage 92.22% 92.08% -0.14%
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Files 184 183 -1
Lines 24141 23670 -471
Branches 3123 3083 -40
===========================================
- Hits 22263 21797 -466
+ Misses 1813 1808 -5
Partials 65 65
Continue to review full report at Codecov.
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Could be backported to 1.0.1 via PR #2798. |
orbeckst
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Jul 3, 2020
* Make the TPR parser a bit faster A function in the TPR parser calls list.pop thousands of times, which is slow. This commit avoids that exansive call. Taking the TPR from https://github.com/bioexcel/covid_modelling_simulation_data/tree/master/spike_protein/full_spike/trimer the parsing time on my computer goes from 25.6s to 9.39s. On a more pathological TPR file, it goes from 3 minutes to about 6s. * Update changelog for #2804 Co-authored-by: Richard Gowers <richardjgowers@gmail.com>
orbeckst
pushed a commit
that referenced
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Jul 12, 2020
* Make the TPR parser a bit faster A function in the TPR parser calls list.pop thousands of times, which is slow. This commit avoids that exansive call. Taking the TPR from https://github.com/bioexcel/covid_modelling_simulation_data/tree/master/spike_protein/full_spike/trimer the parsing time on my computer goes from 25.6s to 9.39s. On a more pathological TPR file, it goes from 3 minutes to about 6s. * Update changelog for #2804 Co-authored-by: Richard Gowers <richardjgowers@gmail.com>
PicoCentauri
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Mar 30, 2021
* Make the TPR parser a bit faster A function in the TPR parser calls list.pop thousands of times, which is slow. This commit avoids that exansive call. Taking the TPR from https://github.com/bioexcel/covid_modelling_simulation_data/tree/master/spike_protein/full_spike/trimer the parsing time on my computer goes from 25.6s to 9.39s. On a more pathological TPR file, it goes from 3 minutes to about 6s. * Update changelog for MDAnalysis#2804 Co-authored-by: Richard Gowers <richardjgowers@gmail.com>
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A function in the TPR parser calls list.pop thousands of times, which is
slow. This commit avoids that exansive call.
Taking the TPR from
https://github.com/bioexcel/covid_modelling_simulation_data/tree/master/spike_protein/full_spike/trimer
the parsing time on my computer goes from 25.6s to 9.39s. On a more
pathological TPR file, it goes from 3 minutes to about 6s.
Changes made in this Pull Request:
PR Checklist
- [ ] Tests?- [ ] Docs?